Workflow file for this run
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| name: Check and test upstream releases or updates | |
| on: | |
| workflow_dispatch: | |
| push: | |
| pull_request: # tests whether it is working on PR | |
| paths: | |
| - '.github/workflows/test_releases.yml' | |
| schedule: | |
| - cron: "0 0 1,15 * *" # Run the workflow on the 1st and 15th day of each month | |
| permissions: | |
| contents: write | |
| pages: write | |
| id-token: write | |
| issues: write | |
| jobs: | |
| ################################ChEBI########################### | |
| check_new_data_chebi: | |
| runs-on: ubuntu-latest | |
| name: Check ChEBI | |
| outputs: | |
| RELEASE_NUMBER: ${{ steps.check_download.outputs.RELEASE_NUMBER }} | |
| CURRENT_RELEASE_NUMBER: ${{ steps.check_download.outputs.CURRENT_RELEASE_NUMBER }} | |
| NEW_RELEASE: ${{ steps.check_download.outputs.NEW_RELEASE }} | |
| DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }} | |
| DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check release date | |
| id: check_download | |
| run: bash scripts/check_release_date.sh chebi | |
| test_sdf_processing_chebi: | |
| name: Test and diff ChEBI | |
| if: needs.check_new_data.outputs.NEW_RELEASE | |
| needs: check_new_data_chebi | |
| env: | |
| RELEASE_NUMBER: ${{ needs.check_new_data_chebi.outputs.RELEASE_NUMBER }} | |
| DATE_OLD: ${{ needs.check_new_data_chebi.outputs.DATE_OLD }} | |
| DATE_NEW: ${{ needs.check_new_data_chebi.outputs.DATE_NEW }} | |
| CURRENT_RELEASE_NUMBER: ${{ needs.check_new_data_chebi.outputs.CURRENT_RELEASE_NUMBER }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.1' # Specify the R version | |
| include-recommended: true | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '11' | |
| distribution: 'temurin' | |
| - name: Download and test new release data | |
| run: bash scripts/test_new_release.sh chebi | |
| - name: Diff ChEBI | |
| if: | |
| ${{ env.FAILED == 'false' }} | |
| run: bash scripts/diff_release.sh chebi | |
| - name: 'Upload ChEBI artifact' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: chebi_processed | |
| path: datasources/chebi/recentData/* | |
| - uses: JasonEtco/create-an-issue@v2 | |
| if: ${{ env.COUNT != 0 }} | |
| name: Post issue about ChEBI update availability | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: ChEBI | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md | |
| update_existing: true | |
| - uses: JasonEtco/create-an-issue@v2 | |
| name: Post issue about ChEBI failing test | |
| if: ${{ env.FAILED == 'true' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: ChEBI | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md | |
| update_existing: true | |
| ################################HGNC########################### | |
| check_new_data_hgnc: | |
| runs-on: ubuntu-latest | |
| name: Check HGNC | |
| outputs: | |
| COMPLETE_NEW: ${{ steps.check_download.outputs.COMPLETE_NEW }} | |
| WITHDRAWN_NEW: ${{ steps.check_download.outputs.WITHDRAWN_NEW }} | |
| DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }} | |
| DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check release date | |
| id: check_download | |
| run: bash scripts/check_release_date.sh hgnc | |
| test_processing_hgnc: | |
| name: Test and diff HGNC | |
| needs: check_new_data_hgnc | |
| env: | |
| DATE_OLD: ${{ needs.check_new_data_hgnc.outputs.DATE_OLD }} | |
| DATE_NEW: ${{ needs.check_new_data_hgnc.outputs.DATE_NEW }} | |
| COMPLETE_NEW: ${{ needs.check_new_data_hgnc.outputs.COMPLETE_NEW }} | |
| WITHDRAWN_NEW: ${{ needs.check_new_data_hgnc.outputs.WITHDRAWN_NEW }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.1' # Specify the R version | |
| include-recommended: true | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '11' | |
| distribution: 'temurin' | |
| - name: Download and test new release data | |
| run: bash scripts/test_new_release.sh hgnc | |
| - name: Diff HGNC | |
| if: | |
| ${{ env.FAILED == 'false' }} | |
| run: bash scripts/diff_release.sh hgnc | |
| - name: 'Upload HGNC artifact' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: hgnc_processed | |
| path: datasources/hgnc/recentData/* | |
| - uses: JasonEtco/create-an-issue@v2 | |
| if: ${{ env.COUNT != 0 }} | |
| name: Post issue about HGNC update availability | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: HGNC | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md | |
| update_existing: true | |
| - uses: JasonEtco/create-an-issue@v2 | |
| name: Post issue about HGNC failing test | |
| if: ${{ env.FAILED == 'true' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: HGNC | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md | |
| update_existing: true | |
| ################################HMDB########################### | |
| check_new_data_hmdb: | |
| runs-on: ubuntu-latest | |
| name: Check HMDB | |
| outputs: | |
| DATE_NEW: ${{ steps.check_new_data_hmdb.outputs.DATE_NEW }} | |
| DATE_OLD: ${{ steps.check_new_data_hmdb.outputs.DATE_OLD }} | |
| NEW_RELEASE: ${{ steps.check_new_data_hmdb.outputs.NEW_RELEASE }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check release date | |
| id: check_download | |
| run: bash scripts/check_release_date.sh hmdb | |
| test_processing_hmdb: | |
| name: Test and diff HMDB | |
| needs: check_new_data_hmdb | |
| env: | |
| DATE_OLD: ${{ needs.check_download.outputs.DATE_OLD }} | |
| DATE_NEW: ${{ needs.check_download.outputs.DATE_NEW }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.1' # Specify the R version | |
| include-recommended: true | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '11' | |
| distribution: 'temurin' | |
| - name: Download and test new release data | |
| run: bash scripts/test_new_release.sh hmdb | |
| - name: Diff HMDB | |
| if: | |
| ${{ env.FAILED == 'false' }} | |
| run: bash scripts/diff_release.sh hmdb | |
| - name: 'Upload HMDB artifact' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: hmdb_processed | |
| path: datasources/hgnc/recentData/* | |
| - uses: JasonEtco/create-an-issue@v2 | |
| if: ${{ env.COUNT != 0 }} | |
| name: Post issue about HGNC update availability | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: HMDB | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md | |
| update_existing: true | |
| - uses: JasonEtco/create-an-issue@v2 | |
| name: Post issue about HGNC failing test | |
| if: ${{ env.FAILED == 'true' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: HMDB | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md | |
| update_existing: true | |
| ################################NCBI########################### | |
| check_new_data_ncbi: | |
| runs-on: ubuntu-latest | |
| name: Check NCBI | |
| outputs: | |
| DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }} | |
| DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check release date | |
| id: check_download | |
| run: bash scripts/check_release_date.sh ncbi | |
| test_processing_ncbi: | |
| name: Test and diff NCBI | |
| needs: check_new_data_ncbi | |
| env: | |
| DATE_OLD: ${{ needs.check_new_data_ncbi.outputs.DATE_OLD }} | |
| DATE_NEW: ${{ needs.check_new_data_ncbi.outputs.DATE_NEW }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.1' # Specify the R version | |
| include-recommended: true | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '11' | |
| distribution: 'temurin' | |
| - name: Download and test new release data | |
| run: | | |
| echo New date $DATE_NEW | |
| bash scripts/test_new_release.sh ncbi | |
| - name: Diff NCBI | |
| if: | |
| ${{ env.FAILED == 'false' }} | |
| run: bash scripts/diff_release.sh ncbi | |
| - uses: JasonEtco/create-an-issue@v2 | |
| if: ${{ env.COUNT != 0 }} | |
| name: Post issue about NCBI update availability | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: NCBI | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md | |
| update_existing: true | |
| - uses: JasonEtco/create-an-issue@v2 | |
| name: Post issue about NCBI failing test | |
| if: ${{ env.FAILED == 'true' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: NCBI | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md | |
| update_existing: true | |
| ##############################UNIPROT######################### | |
| check_new_data_uniprot: | |
| runs-on: ubuntu-latest | |
| name: Check UniProt | |
| outputs: | |
| UNIPROT_SPROT_NEW: ${{ steps.check_download.outputs.UNIPROT_SPROT_NEW }} | |
| SEC_AC_NEW: ${{ steps.check_download.outputs.SEC_AC_NEW }} | |
| DELAC_SP_NEW: ${{ steps.check_download.outputs.DELAC_SP_NEW }} | |
| DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }} | |
| DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check release date | |
| id: check_download | |
| run: bash scripts/check_release_date.sh uniprot | |
| test_processing_uniprot: | |
| name: Test and diff UniProt | |
| needs: check_new_data_uniprot | |
| env: | |
| DATE_OLD: ${{ needs.check_new_data_uniprot.outputs.DATE_OLD }} | |
| DATE_NEW: ${{ needs.check_new_data_uniprot.outputs.DATE_NEW }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.1' # Specify the R version | |
| include-recommended: true | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '11' | |
| distribution: 'temurin' | |
| - name: Download and test new release data | |
| run: bash scripts/test_new_release.sh uniprot | |
| - name: Diff UniProt | |
| if: | |
| ${{ env.FAILED == 'false' }} | |
| run: bash scripts/diff_release.sh uniprot | |
| - uses: JasonEtco/create-an-issue@v2 | |
| if: ${{ env.COUNT != 0 }} | |
| name: Post issue about UniProt update availability | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: UniProt | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md | |
| update_existing: true | |
| - uses: JasonEtco/create-an-issue@v2 | |
| name: Post issue about UniProt failing test | |
| if: ${{ env.FAILED == 'true' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SOURCE: UniProt | |
| with: | |
| filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md | |
| update_existing: true | |
| #trigger-docker-update: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v4 | |
| # - name: Trigger docker release | |
| # uses: peter-evans/repository-dispatch@v3 | |
| # with: | |
| # token: ${{ secrets.pat_external_workflow }} | |
| # repository: jmillanacosta/omicsFixID | |
| # event-type: update-event |